PfizerFragmenter

pydantic model openff.qcsubmit.workflow_components.PfizerFragmenter[source]

The openff.fragmenter implementation of the Pfizer fragmenation method as described here (doi: 10.1021/acs.jcim.9b00373)

Show JSON schema

{
   "title": "PfizerFragmenter",
   "description": "The openff.fragmenter implementation of the Pfizer fragmenation method as described here\n(doi: 10.1021/acs.jcim.9b00373)",
   "type": "object",
   "properties": {
      "type": {
         "title": "Type",
         "default": "PfizerFragmenter",
         "enum": [
            "PfizerFragmenter"
         ],
         "type": "string"
      },
      "target_torsion_smarts": {
         "title": "Target Torsion Smarts",
         "description": "The list of SMARTS patterns used to identify central target bonds to fragment around. By default this is any single non-termial bond.",
         "type": "array",
         "items": {
            "type": "string"
         }
      }
   }
}

Config

allow_mutation: bool = True
validate_assignment: bool = True

Fields

target_torsion_smarts (Optional[List[str]])
type (Literal['PfizerFragmenter'])

Validators

check_environments » target_torsion_smarts

field type: Literal['PfizerFragmenter'] = 'PfizerFragmenter'

classmethod description()[source]

Returns a friendly description of the workflow component.

Return type: str

apply(molecules, toolkit_registry, processors=None, verbose=True)

This is the main feature of the workflow component which should accept a molecule, perform the component action and then return any resulting molecules.

Parameters

molecules (List[openff.toolkit.topology.molecule.Molecule]) – The list of molecules to be processed by this component.
toolkit_registry (openff.toolkit.utils.toolkit_registry.ToolkitRegistry) – The openff.toolkit.utils.ToolkitRegistry which declares the available backend toolkits to be used.
processors (Optional[int]) – The number of processor the component can use to run the job in parallel across molecules, None will default to all cores.
verbose (bool) – If true a progress bar should be shown on screen.

Returns

A component result class which handles collecting together molecules that pass and fail the component

Return type

openff.qcsubmit.workflow_components.utils.ComponentResult

classmethod fail_reason()

Returns a friendly description of why a molecule would fail to pass the component.

Return type: str

classmethod info()

Returns a dictionary of the friendly descriptions of the class.

Return type: Dict[str, str]

classmethod is_available()

Check if fragmenter can be imported.

Return type: bool

classmethod properties()

Returns the runtime properties of the component such as parallel safe.

Return type: openff.qcsubmit.common_structures.ComponentProperties

provenance(toolkit_registry)

Collect the toolkit information and add the fragmenter version information.

Parameters: toolkit_registry (openff.toolkit.utils.toolkit_registry.ToolkitRegistry) –
Return type: Dict

field target_torsion_smarts: Optional[List[str]] = None

The list of SMARTS patterns used to identify central target bonds to fragment around. By default this is any single non-termial bond.

Validated by

check_environments